A systematic comparison of genome-scale clustering algorithms

BMC Bioinformatics

Table 3 Runtimes for each clustering method

Parameters used to produce the best Jaccard score, and the associated runtime for the given method and parameters are displayed. Specific parameter descriptions are listed in Table 1. MeV times were reported by GUI results. Hierarchical methods use the "flashClust" package for R, which is a C++ implementation of the standard "hclust" package. Hierarchical timings do not include the time for tree cutting (which is negligible). flashClust and WGCNA packages were downloaded from the CRAN repository June 22, 2011. Versions reported refer to the version used for runtime calculation; in some cases, previous versions were used to generate clusters for scoring. r = rectangular, h = hexagonal. *A GUI-based graphical tool which is no longer maintained was used to generate clusters for Jaccard scoring while the latest R implementation was using in timing, **Total elapsed time reported by the system.

ISSN: 1471-2105